alive-research / slicer-liveranalysis Goto Github PK

Hello @RafaelPalomar and everyone!

I was updating the extension for different liver volume and segmentation (than the default ones LiverVolume000 and LiverSegmentation000). You can check the changes I have made so far here.
I am able now to select any segmentations and create the respective models, but I have the following error when I try to perform one of the Resection Slicing Contour:
Error in AddResectionSlicingContour: invalid internal target parenchyma

Could I have some guidance, please? I attached the node information of the target parenchyma I am using.

Thank you in advance for any help you could provide

This covers the development of a Slicing contour markup that will help initializing the resection.

TODO:

• Slicing Contour MRMLNode
• Slicing Contour MRMLDisplayNode
• Slicing Contour MRMLStoreNode
• Slicing Contour VTKWidget
• Slicing Contour 3DRepresentation
• Slicing Contour 2DRepresentation
• Slicing Contour qtAdditionalWidget
• Slicing Contour Integration (module, logic, widgets)
• Unit Testing
• Integration Testing

Add BezierSurfaceSource, and fix Windows linking errors

This is to test the capabilities of the new Pluggable Markups infrastructure in Python. Use our custom Slicer.

• Create a vtkSlicerWidget.
• Create a vtkSlicerWidgetRepresentation
• Create a vtkMRMLMarkupsNode
• Register the components and test

CircleCI will run based on the configuration found on .circleci in the root of the project. A good starting point for this should be the .circleci file already include on Slicer. Most likely, the Slicer .circleci file will be using a container with the required environment; this environment will not directly be useful, because we need a container with the slicer source built already to save the computations required to build Slicer.

The project needs to be registered in CircleCI. I believe login to CircleCI through Github OAuth will let any developer to set up the project in CircleCI

• Enable tests. Either create a Docker image with X support or only create tests that don't need X

The aim of this is the creation of a resection widget based on Bezier deformable surfaces. We are basing this development on the pluggable-markups branch. For an example of the working demo of the NorMIT-Plan, see the following video:

[NorMIT-Plan demo](https://youtu.be/7M3DULQp81k

The part to implement here is only the deformable Bezier surface. The initialization part (slicing contour) is considered in #5. Technical details are given in this paper. There is code available in NorMIT-Plan. Note that some parts of the code cannot be integrated directly, since they are not using modern infrastructure in 3D Slicer (e.g., Markups). Suggestion of sub-tasks and order:

• Add a basic vtkMRMLMarkupsNode (this is just to support the development).
• Transfer the vtkBezierSurfaceSource code to the Slicer module (this should not require any adaptation).
• Create the 3D widget representation. (Look of the widget).
• Create the 3D widget. (Interaction of the widget).
• Adding unit tests.
• Adding integration tests.
• Create the 2D widget representation. (Look of the widget).
• Create the 2D widget. (Interaction of the widget).

One might have to register a dummy widget and markups in order to see the results on the screen. For a working example look at the line widget already existing line-widget.

Bezier surfaces are complex to compute and have global knot support (a change of a control point changes the whole surface). We want to change to resection surfaces with local support and more efficient to compute.